First Description of a Satellite DNA in Manatees’ Centromeric Regions

Abstract

Trichechus manatus and Trichechus inunguis are the two Sirenia species that occur in the Americas. Despite their increasing extinction risk, many aspects of their biology remain understudied, including the repetitive DNA fraction of their genomes. Here we used the sequenced genome of T. manatus and TAREAN to identify satellite DNAs (satDNAs) in this species. We report the first description of TMAsat, a satDNA comprising ~0.87% of the genome, with ~684bp monomers and centromeric localization. In T. inunguis, TMAsat showed similar monomer length, chromosome localization and conserved CENP-B box-like motifs as in T. manatus. We also detected this satDNA in the Dugong dugon and in the now extinct Hydrodamalis gigas genomes. The neighbor-joining tree shows that TMAsat sequences from T. manatus, T. inunguis, D. dugon, and H. gigas lack species-specific clusters, which disagrees with the predictions of concerted evolution. We detected a divergent TMAsat-like homologous sequence in elephants and hyraxes, but not in other mammals, suggesting this sequence was already present in the common ancestor of Paenungulata, and later became a satDNA in the Sirenians. This is the first description of a centromeric satDNA in manatees and will facilitate the inclusion of Sirenia in future studies of centromeres and satDNA biology.

Karyotypical Confirmation of Natural Hybridization between Two Manatee Species, Trichechus manatus and Trichechus inunguis

“…Unfortunately, we could not analyze the distribution of these sequences in the T. inunguis species due the low number of metaphases obtained. The distribution of microsatellite sequences in the karyotype of manatees is still poorly studied, with only one previous report showing the characterization and distribution of one satellite sequence in T. manatus and T. inunguis [ 32 ]. Nevertheless, our results indicate that microsatellites could represent useful markers for the detection of heterozygous chromosome pairs.…”

Karyotypes of Manatees: New Insights into Hybrid Formation (Trichechus inunguis × Trichechus m. manatus) in the Amazon Estuary

“…), satellite DNAs, microsatellites, and transposable elements [ 12 ]. In the Trichechus genome, the centromeric satellite DNA TMAsat [ 12 , 13 ], microsatellites [ 9 ], and the mobile element Long Interspersed Nuclear Element (LINE-1) [ 14 ] were previously identified (and mapped in chromosomes). The genomic shock caused by the union of genomes in interspecific hybrids can promote changes in gene expression, the occurrence of chromosomal rearrangements, and epigenetic alterations [ 15 ].…”

Population Scale Analysis of Centromeric Satellite DNA Reveals Highly Dynamic Evolutionary Patterns and Genomic Organization in Long-Tailed and Rhesus Macaques

“…Although the potential impact of the variations in the centromeric sequences and their associated satellites on the functions of centromeres and heterochromatin has been recognized, their study remains difficult [ 118 ]. However, the recent integration of bioinformatics and cytogenetics as chromosomics has greatly assisted the assessment of repeat variations [ 119 , 120 ]. These combined approaches offer deep insights into the organization of cen-satDNA within primate genomes, thus facilitating our understanding of their possible roles in adaptive evolution at the population level and highlighting the extraordinary diversification of tandem repeats.…”